Rhythmic F12SE setup using line in

Well, regardless of the online instructions it sounds like either your crossover is set too high or the volume is set too high, or both. So I’d first play with turning those two settings down first and see what that does, and then try altering the phase to see if that can improve things further. The other thought is that your sub is not placed optimally in your room that the prior room correction software was compensating for, so you may need to experiment with sub placement in addition to adjusting the sub’s controls. Here are two helpful links to address both issues I recently posted on another thread that may be helpful for you too…

First, if you haven’t already, use the “crawl method” to find the best location(s) for the sub(s) in your room for best bass…
https://www.audioholics.com/home-theater-connection/crawling-for-bass-subwoofer-placement

Then use this to fine tune your sub’s individual controls…
https://lifehacker.com/how-to-properly-set-your-subwoofers-volume-without-sh-1506136549

Using these techniques should give you a high degree of confidence that your subs are dialed in well. Hope this helps, and best of luck.

I would suggest doing one thing at a time.  Sometimes adding port plugs can change the sound characteristics of the speakers, so I’d definitely try that last after everything else is dialed in.